In a discovery that could redefine how we understand cellular resilience and adaptability, Scripps Research scientists have uncovered the secret interactions between a primordial inorganic phosphate polymer known as polyphosphate (polyP) and two building blocks of life: DNA and the element magnesium. . These components formed groups of small liquid droplets – also known as condensates – with flexible and adaptable structures.
PolyP and magnesium participate in many biological processes. The findings could therefore lead to new methods for fine-tuning cellular responses, which could have impactful applications in translational medicine.
The resulting study, published in Nature Communications On October 26, 2024, it reveals a delicate “Goldilocks” zone, a specific magnesium concentration range, where DNA envelopes polyP-magnesium ion condensates. Similar to a thin eggshell covering a liquid-like interior, this seemingly simple structure can help cells organize and protect their genetic material.
This work began as a collaboration between co-senior authors Associate Professor Lisa Racki, PhD, and Professor Ashok Deniz, PhD, both in the Department of Computational and Integrative Structural Biology at Scripps Research. Racki had been studying these structures in bacterial cells, while Deniz’s adjacent lab was exploring the physical chemistry of biomolecular condensates for the past decade. They realized that collaboration was the only way to unlock these ancient interactions.
“We knew that the DNA was very close to the magnesium-rich polyp condensates in the cells, but we were totally surprised by the beautiful spheres of DNA that lit up under the microscope,” says Racki.
“As molecular detectives, seeing these structures raised interesting questions for us about the physics and mathematics of the DNA layers and whether they influenced the polyp condensates,” adds Deniz.
Their microscopy images revealed that the DNA is wrapped around a condensate, creating a thin barrier similar to an eggshell. This layer could affect the transport of molecules and also slow down fusion – the process in which two condensates merge into one. Without the DNA layers, polyP-magnesium ion condensates fuse easily, like oil droplets and vinegar fuse in a bottle of salad dressing when shaken.
However, careful examination showed that fusion was generally slowed to varying degrees, depending on the length of the DNA. The researchers suspected that longer DNA caused more tangling on condensate surfaces, similar to how long hair tangles more than short hair.
DNA is more than 1,000 times thinner in diameter than condensates, making it difficult to visualize molecular details. Fortunately, two other Scripps Research faculty members have developed the infrastructure to capture such images: Assistant Professor Danielle Grotjahn, PhD, and Scripps Donghyun Fellow Raphael Park, PhD.
Teaming with Park and with help from Grotjahn, the researchers used cryo-electron tomography to closely examine the surfaces of the condensate. Using electrons instead of light, this technique captures high-resolution three-dimensional images of samples that have been quickly frozen to preserve their structures. The new images revealed that the DNA forms filaments that protrude from the surfaces of the condensate, resembling tangled hairs.
Another crucial discovery: the formation of the DNA shell only occurred within a specific magnesium concentration range: too much or too little, and the shell would not materialize. This “Goldilocks” effect highlights how cells can regulate condensate structure, size, and function simply by adjusting control parameters.
“Although we think of cellular interfaces as boundaries, they also create a new landscape by providing a surface for molecules to organize,” Racki notes. “It’s possible that the DNA isn’t actually a tangled mess on the surface, but rather is organized by these condensates.”
In this context, Deniz and Racki are particularly interested in understanding DNA supercoiling: how DNA twists like a spring to fit inside cells.
“Cells have to manage the loops of their DNA,” explains Racki. “Interestingly, the mathematics of DNA supercoiling results in ‘action at a distance’ effects, like how twisting a rope can create coils far from where you hold it.”
The researchers suspect that DNA interactions with polyp condensates in cells could propagate local changes in DNA supercoiling over long distances, leading to broader changes in gene expression and cellular function. Investigating this effect is one of the team’s next objectives.
“We are excited by the prospects of harnessing these discoveries to develop new tools for cell control: potentially simpler and more cost-effective approaches to managing biomatter for biomedicine,” says Deniz.
In addition to Deniz, Racki, Grotjahn and Park, authors of the study, “Reentrant DNA layers adjust the size of the polyphosphate condensate“, include co-authors Ravi Chawla and Jenna KA Tom, and Tumara Boyd, Nicholas H. Tu and Tanxi Bai of Scripps Research.
This work was supported by funds from the National Institutes of Health (NIGMS Grant R35 GM130375, Grant DP2-GM-739-140918 and S10OD032467), seed funds from Scripps Research, a postdoctoral fellowship from the American Heart Association (Award #903967), and the Pew Scholars Program.